What to do with duplicate Innovations in a genome?
Because this is more of an answer than a comment:


  In the add connection
  mutation, a single new connection gene with a random weight is added connecting
  two previously unconnected nodes. 


So two nodes that have been mutated with a connection, can't remutate because the nodes should be unconnected.


  In the add node mutation, an existing connection is
  split and the new node placed where the old connection used to be. The old connection
  is disabled and two new connections are added to the genome.


The old connection is disabled, so the same mutation can't occur again on this connection. In practice, you can just remove the disabled connection, because it will be formed again with the add connection mutation.